diff --git a/build/gen.py b/build/gen.py
index ee4f8e14..89714678 100755
--- a/build/gen.py
+++ b/build/gen.py
@@ -332,8 +332,11 @@ def WriteGNNinja(path, platform, host, options):
       ldflags.extend(['-maix64', '-pthread'])
 
     if options.use_lto:
-      cflags.extend(['-flto', '-fwhole-program-vtables'])
-      ldflags.extend(['-flto', '-fwhole-program-vtables'])
+      cflags.append('-flto')
+      ldflags.append('-flto')
+      if "clang" in cc:
+        cflags.append('-fwhole-program-vtables')
+        ldflags.append('-fwhole-program-vtables')
 
   elif platform.is_msvc():
     if not options.debug: